Starting phenix.real_space_refine on Fri Jul 25 02:32:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p3f_13179/07_2025/7p3f_13179_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p3f_13179/07_2025/7p3f_13179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p3f_13179/07_2025/7p3f_13179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p3f_13179/07_2025/7p3f_13179.map" model { file = "/net/cci-nas-00/data/ceres_data/7p3f_13179/07_2025/7p3f_13179_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p3f_13179/07_2025/7p3f_13179_neut.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 124 5.49 5 S 32 5.16 5 C 3858 2.51 5 N 1280 2.21 5 O 1580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6878 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1145 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "B" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1145 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "F" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1028 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "R" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1022 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' ZN': 1, 'ATP': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' ZN': 1, 'ATP': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24 SG CYS A 3 103.479 45.542 34.915 1.00 72.57 S ATOM 48 SG CYS A 6 106.815 43.750 34.928 1.00 73.80 S ATOM 254 SG CYS A 31 106.328 46.744 32.620 1.00 72.42 S ATOM 275 SG CYS A 34 104.522 43.517 31.897 1.00 75.24 S ATOM 2314 SG CYS B 3 38.685 14.665 40.459 1.00 71.45 S ATOM 2338 SG CYS B 6 40.204 11.612 38.607 1.00 68.82 S ATOM 2544 SG CYS B 31 36.880 12.614 37.317 1.00 74.44 S ATOM 2565 SG CYS B 34 37.290 11.235 41.007 1.00 77.60 S Restraints were copied for chains: C, D Time building chain proxies: 5.69, per 1000 atoms: 0.83 Number of scatterers: 6878 At special positions: 0 Unit cell: (129.31, 90.45, 75.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 32 16.00 P 124 15.00 O 1580 8.00 N 1280 7.00 C 3858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 44 " distance=0.00 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 71 " distance=0.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 783.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 203 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 34 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 6 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 3 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 31 " pdb=" ZN B 203 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 6 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 34 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 3 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 31 " pdb=" ZN C 203 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 6 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 3 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 31 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 34 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 6 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 31 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 34 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 3 " Number of angles added : 24 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1112 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 6 sheets defined 51.0% alpha, 16.7% beta 41 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.666A pdb=" N VAL A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 95 removed outlier: 3.720A pdb=" N THR A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 removed outlier: 3.605A pdb=" N GLY A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 107 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 4.289A pdb=" N GLU A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.936A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.727A pdb=" N PHE A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.666A pdb=" N VAL C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 95 removed outlier: 3.720A pdb=" N THR C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 117 removed outlier: 3.605A pdb=" N GLY C 106 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU C 107 " --> pdb=" O HIS C 103 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Proline residue: C 112 - end of helix removed outlier: 4.289A pdb=" N GLU C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 removed outlier: 3.936A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 147 removed outlier: 3.727A pdb=" N PHE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 71 removed outlier: 3.699A pdb=" N VAL B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 96 removed outlier: 3.917A pdb=" N THR B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.756A pdb=" N GLY B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix removed outlier: 3.737A pdb=" N GLU B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 4.052A pdb=" N VAL B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 147 removed outlier: 3.602A pdb=" N GLU B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 71 removed outlier: 3.700A pdb=" N VAL D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 96 removed outlier: 3.917A pdb=" N THR D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY D 96 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 removed outlier: 3.756A pdb=" N GLY D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Proline residue: D 112 - end of helix removed outlier: 3.737A pdb=" N GLU D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 removed outlier: 4.052A pdb=" N VAL D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 147 removed outlier: 3.601A pdb=" N GLU D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 20 removed outlier: 5.258A pdb=" N VAL A 13 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLN A 30 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 24 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 41 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 43 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 43 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL D 41 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ARG D 26 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER D 16 " --> pdb=" O ARG D 26 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG D 28 " --> pdb=" O VAL D 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 57 removed outlier: 6.172A pdb=" N MET A 47 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 12 through 20 removed outlier: 5.257A pdb=" N VAL C 13 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLN C 30 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER C 24 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C 41 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 43 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 43 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 41 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ARG B 26 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER B 16 " --> pdb=" O ARG B 26 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG B 28 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 55 through 57 removed outlier: 6.172A pdb=" N MET C 47 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AA6, first strand: chain 'D' and resid 55 through 57 214 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 954 1.31 - 1.44: 2264 1.44 - 1.56: 3706 1.56 - 1.69: 238 1.69 - 1.81: 40 Bond restraints: 7202 Sorted by residual: bond pdb=" CA SER A 133 " pdb=" CB SER A 133 " ideal model delta sigma weight residual 1.532 1.455 0.077 1.56e-02 4.11e+03 2.44e+01 bond pdb=" CA SER C 133 " pdb=" CB SER C 133 " ideal model delta sigma weight residual 1.532 1.455 0.077 1.56e-02 4.11e+03 2.42e+01 bond pdb=" CA ALA A 140 " pdb=" CB ALA A 140 " ideal model delta sigma weight residual 1.528 1.458 0.070 1.56e-02 4.11e+03 2.03e+01 bond pdb=" CA ALA C 140 " pdb=" CB ALA C 140 " ideal model delta sigma weight residual 1.528 1.459 0.070 1.56e-02 4.11e+03 2.00e+01 bond pdb=" C PHE A 131 " pdb=" O PHE A 131 " ideal model delta sigma weight residual 1.235 1.185 0.050 1.15e-02 7.56e+03 1.87e+01 ... (remaining 7197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 9087 2.06 - 4.12: 971 4.12 - 6.19: 129 6.19 - 8.25: 33 8.25 - 10.31: 6 Bond angle restraints: 10226 Sorted by residual: angle pdb=" PB ATP B 201 " pdb=" O3B ATP B 201 " pdb=" PG ATP B 201 " ideal model delta sigma weight residual 139.87 131.73 8.14 1.00e+00 1.00e+00 6.62e+01 angle pdb=" PB ATP D 201 " pdb=" O3B ATP D 201 " pdb=" PG ATP D 201 " ideal model delta sigma weight residual 139.87 131.75 8.12 1.00e+00 1.00e+00 6.60e+01 angle pdb=" PB DTP B 202 " pdb=" O3B DTP B 202 " pdb=" PG DTP B 202 " ideal model delta sigma weight residual 139.87 131.80 8.07 1.00e+00 1.00e+00 6.52e+01 angle pdb=" PB DTP D 202 " pdb=" O3B DTP D 202 " pdb=" PG DTP D 202 " ideal model delta sigma weight residual 139.87 131.82 8.05 1.00e+00 1.00e+00 6.49e+01 angle pdb=" PB DTP C 202 " pdb=" O3B DTP C 202 " pdb=" PG DTP C 202 " ideal model delta sigma weight residual 139.87 132.55 7.32 1.00e+00 1.00e+00 5.36e+01 ... (remaining 10221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.18: 3414 28.18 - 56.36: 691 56.36 - 84.53: 114 84.53 - 112.71: 5 112.71 - 140.89: 2 Dihedral angle restraints: 4226 sinusoidal: 2522 harmonic: 1704 Sorted by residual: dihedral pdb=" C GLU D 42 " pdb=" N GLU D 42 " pdb=" CA GLU D 42 " pdb=" CB GLU D 42 " ideal model delta harmonic sigma weight residual -122.60 -112.04 -10.56 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" C GLU B 42 " pdb=" N GLU B 42 " pdb=" CA GLU B 42 " pdb=" CB GLU B 42 " ideal model delta harmonic sigma weight residual -122.60 -112.09 -10.51 0 2.50e+00 1.60e-01 1.77e+01 dihedral pdb=" C THR C 19 " pdb=" N THR C 19 " pdb=" CA THR C 19 " pdb=" CB THR C 19 " ideal model delta harmonic sigma weight residual -122.00 -132.37 10.37 0 2.50e+00 1.60e-01 1.72e+01 ... (remaining 4223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 846 0.074 - 0.147: 229 0.147 - 0.220: 62 0.220 - 0.293: 15 0.293 - 0.367: 4 Chirality restraints: 1156 Sorted by residual: chirality pdb=" CA THR C 19 " pdb=" N THR C 19 " pdb=" C THR C 19 " pdb=" CB THR C 19 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA THR A 19 " pdb=" N THR A 19 " pdb=" C THR A 19 " pdb=" CB THR A 19 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA ILE A 141 " pdb=" N ILE A 141 " pdb=" C ILE A 141 " pdb=" CB ILE A 141 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1153 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP D 201 " -0.096 2.00e-02 2.50e+03 4.13e-02 4.69e+01 pdb=" C2 ATP D 201 " 0.014 2.00e-02 2.50e+03 pdb=" C4 ATP D 201 " 0.030 2.00e-02 2.50e+03 pdb=" C5 ATP D 201 " 0.024 2.00e-02 2.50e+03 pdb=" C6 ATP D 201 " -0.005 2.00e-02 2.50e+03 pdb=" C8 ATP D 201 " 0.029 2.00e-02 2.50e+03 pdb=" N1 ATP D 201 " -0.004 2.00e-02 2.50e+03 pdb=" N3 ATP D 201 " 0.030 2.00e-02 2.50e+03 pdb=" N6 ATP D 201 " -0.070 2.00e-02 2.50e+03 pdb=" N7 ATP D 201 " 0.031 2.00e-02 2.50e+03 pdb=" N9 ATP D 201 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP B 201 " 0.096 2.00e-02 2.50e+03 4.12e-02 4.66e+01 pdb=" C2 ATP B 201 " -0.014 2.00e-02 2.50e+03 pdb=" C4 ATP B 201 " -0.030 2.00e-02 2.50e+03 pdb=" C5 ATP B 201 " -0.024 2.00e-02 2.50e+03 pdb=" C6 ATP B 201 " 0.005 2.00e-02 2.50e+03 pdb=" C8 ATP B 201 " -0.029 2.00e-02 2.50e+03 pdb=" N1 ATP B 201 " 0.005 2.00e-02 2.50e+03 pdb=" N3 ATP B 201 " -0.030 2.00e-02 2.50e+03 pdb=" N6 ATP B 201 " 0.069 2.00e-02 2.50e+03 pdb=" N7 ATP B 201 " -0.030 2.00e-02 2.50e+03 pdb=" N9 ATP B 201 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 21 " -0.025 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C ASP D 21 " 0.084 2.00e-02 2.50e+03 pdb=" O ASP D 21 " -0.031 2.00e-02 2.50e+03 pdb=" N GLY D 22 " -0.028 2.00e-02 2.50e+03 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1219 2.77 - 3.31: 5907 3.31 - 3.84: 12082 3.84 - 4.37: 15240 4.37 - 4.90: 22227 Nonbonded interactions: 56675 Sorted by model distance: nonbonded pdb=" OG1 THR A 101 " pdb=" OD2 ASP A 104 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR C 101 " pdb=" OD2 ASP C 104 " model vdw 2.242 3.040 nonbonded pdb=" NH1 ARG B 68 " pdb=" OE2 GLU B 78 " model vdw 2.286 3.120 nonbonded pdb=" NH1 ARG D 68 " pdb=" OE2 GLU D 78 " model vdw 2.286 3.120 nonbonded pdb=" O ALA B 70 " pdb=" NH1 ARG B 123 " model vdw 2.420 3.120 ... (remaining 56670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.850 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.195 7218 Z= 0.629 Angle : 1.335 13.022 10252 Z= 0.926 Chirality : 0.077 0.367 1156 Planarity : 0.008 0.049 940 Dihedral : 25.952 140.891 3110 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.59 % Allowed : 5.95 % Favored : 92.46 % Cbeta Deviations : 1.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.35), residues: 580 helix: -0.04 (0.31), residues: 270 sheet: -1.47 (0.55), residues: 96 loop : -1.31 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS B 103 PHE 0.043 0.004 PHE B 38 TYR 0.011 0.002 TYR B 121 ARG 0.008 0.001 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.16887 ( 317) hydrogen bonds : angle 9.31485 ( 832) metal coordination : bond 0.09406 ( 16) metal coordination : angle 4.65050 ( 24) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00932 ( 7202) covalent geometry : angle 1.31782 (10226) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.538 Fit side-chains REVERT: A 17 ARG cc_start: 0.7761 (mmt180) cc_final: 0.7557 (ttp-110) REVERT: A 25 ILE cc_start: 0.8908 (tt) cc_final: 0.8585 (tt) REVERT: A 134 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8141 (pt) REVERT: C 17 ARG cc_start: 0.7739 (mmt180) cc_final: 0.7490 (ttp-110) outliers start: 8 outliers final: 0 residues processed: 132 average time/residue: 0.2551 time to fit residues: 41.4825 Evaluate side-chains 111 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.197194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.133145 restraints weight = 7990.647| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.76 r_work: 0.3382 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7218 Z= 0.169 Angle : 0.608 6.055 10252 Z= 0.350 Chirality : 0.038 0.129 1156 Planarity : 0.005 0.045 940 Dihedral : 28.428 137.923 2012 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.59 % Allowed : 11.71 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.35), residues: 580 helix: 0.32 (0.32), residues: 274 sheet: -1.35 (0.50), residues: 104 loop : -0.93 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 8 PHE 0.010 0.001 PHE A 137 TYR 0.015 0.003 TYR B 121 ARG 0.004 0.000 ARG B 123 Details of bonding type rmsd hydrogen bonds : bond 0.06260 ( 317) hydrogen bonds : angle 3.79010 ( 832) metal coordination : bond 0.00664 ( 16) metal coordination : angle 3.18614 ( 24) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00366 ( 7202) covalent geometry : angle 0.58924 (10226) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.805 Fit side-chains REVERT: A 26 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7531 (ttp80) REVERT: A 28 ARG cc_start: 0.9059 (tpt90) cc_final: 0.8785 (tpt90) REVERT: A 42 GLU cc_start: 0.7745 (pt0) cc_final: 0.7363 (pt0) REVERT: C 28 ARG cc_start: 0.9037 (tpt90) cc_final: 0.8756 (tpt90) outliers start: 8 outliers final: 6 residues processed: 113 average time/residue: 0.3906 time to fit residues: 55.9907 Evaluate side-chains 100 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.0870 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.196729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133476 restraints weight = 8088.792| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.04 r_work: 0.3316 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7218 Z= 0.165 Angle : 0.573 5.708 10252 Z= 0.327 Chirality : 0.036 0.118 1156 Planarity : 0.005 0.044 940 Dihedral : 27.761 146.638 2010 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.79 % Allowed : 16.47 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.35), residues: 580 helix: 0.48 (0.32), residues: 272 sheet: -1.19 (0.48), residues: 114 loop : -1.02 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 8 PHE 0.013 0.001 PHE A 124 TYR 0.009 0.002 TYR B 121 ARG 0.005 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.05469 ( 317) hydrogen bonds : angle 3.58753 ( 832) metal coordination : bond 0.00258 ( 16) metal coordination : angle 2.91753 ( 24) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00361 ( 7202) covalent geometry : angle 0.55647 (10226) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.656 Fit side-chains REVERT: A 17 ARG cc_start: 0.8009 (mmt180) cc_final: 0.6764 (ttp-110) REVERT: A 26 ARG cc_start: 0.7608 (ttm-80) cc_final: 0.7339 (mtp-110) REVERT: A 28 ARG cc_start: 0.8887 (tpt90) cc_final: 0.8341 (tpt90) REVERT: A 42 GLU cc_start: 0.7724 (pt0) cc_final: 0.7270 (pt0) REVERT: C 17 ARG cc_start: 0.8107 (mmt180) cc_final: 0.6816 (ttp-110) REVERT: C 28 ARG cc_start: 0.8930 (tpt90) cc_final: 0.8286 (tpt90) REVERT: C 42 GLU cc_start: 0.7455 (pt0) cc_final: 0.6828 (pt0) REVERT: B 30 GLN cc_start: 0.7842 (tt0) cc_final: 0.7150 (tt0) REVERT: D 30 GLN cc_start: 0.7871 (tt0) cc_final: 0.7176 (tt0) outliers start: 9 outliers final: 6 residues processed: 112 average time/residue: 0.3525 time to fit residues: 48.4415 Evaluate side-chains 105 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 122 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 34 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN D 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.193758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127490 restraints weight = 8215.612| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.95 r_work: 0.3180 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7218 Z= 0.220 Angle : 0.606 6.639 10252 Z= 0.335 Chirality : 0.036 0.134 1156 Planarity : 0.005 0.045 940 Dihedral : 28.064 142.195 2010 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.98 % Allowed : 16.27 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.35), residues: 580 helix: 0.28 (0.31), residues: 276 sheet: -0.74 (0.51), residues: 104 loop : -0.92 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 8 PHE 0.016 0.002 PHE A 124 TYR 0.009 0.002 TYR B 121 ARG 0.004 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.05599 ( 317) hydrogen bonds : angle 3.74360 ( 832) metal coordination : bond 0.00411 ( 16) metal coordination : angle 3.30339 ( 24) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00511 ( 7202) covalent geometry : angle 0.58479 (10226) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.595 Fit side-chains REVERT: A 17 ARG cc_start: 0.8214 (mmt180) cc_final: 0.6880 (ttp-110) REVERT: A 28 ARG cc_start: 0.8981 (tpt90) cc_final: 0.8387 (tpt90) REVERT: A 42 GLU cc_start: 0.7816 (pt0) cc_final: 0.7519 (pt0) REVERT: C 17 ARG cc_start: 0.8167 (mmt180) cc_final: 0.6983 (ttp-110) REVERT: C 28 ARG cc_start: 0.8989 (tpt90) cc_final: 0.8720 (tpt90) outliers start: 15 outliers final: 14 residues processed: 113 average time/residue: 0.3909 time to fit residues: 55.9781 Evaluate side-chains 116 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 97 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.0370 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.196518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130343 restraints weight = 8077.216| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.59 r_work: 0.3254 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7218 Z= 0.159 Angle : 0.552 5.945 10252 Z= 0.311 Chirality : 0.034 0.117 1156 Planarity : 0.004 0.043 940 Dihedral : 27.680 145.264 2010 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.38 % Allowed : 17.66 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.36), residues: 580 helix: 0.46 (0.32), residues: 274 sheet: -0.57 (0.52), residues: 104 loop : -0.89 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 8 PHE 0.011 0.001 PHE A 124 TYR 0.009 0.002 TYR D 121 ARG 0.003 0.000 ARG B 123 Details of bonding type rmsd hydrogen bonds : bond 0.05082 ( 317) hydrogen bonds : angle 3.58906 ( 832) metal coordination : bond 0.00273 ( 16) metal coordination : angle 2.81647 ( 24) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00353 ( 7202) covalent geometry : angle 0.53554 (10226) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.861 Fit side-chains REVERT: A 17 ARG cc_start: 0.8180 (mmt180) cc_final: 0.6848 (ttp-110) REVERT: A 28 ARG cc_start: 0.8950 (tpt90) cc_final: 0.8495 (tpt-90) REVERT: A 42 GLU cc_start: 0.7772 (pt0) cc_final: 0.7364 (pt0) REVERT: C 28 ARG cc_start: 0.8943 (tpt90) cc_final: 0.8735 (tpt90) REVERT: B 23 THR cc_start: 0.7665 (p) cc_final: 0.7380 (t) REVERT: B 30 GLN cc_start: 0.7800 (tt0) cc_final: 0.7345 (tt0) REVERT: D 23 THR cc_start: 0.7704 (p) cc_final: 0.7446 (t) REVERT: D 30 GLN cc_start: 0.7761 (tt0) cc_final: 0.7433 (mt0) outliers start: 12 outliers final: 9 residues processed: 113 average time/residue: 0.3375 time to fit residues: 47.7658 Evaluate side-chains 112 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 0.0270 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN B 72 GLN ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.196917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.130756 restraints weight = 8075.030| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.92 r_work: 0.3234 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7218 Z= 0.160 Angle : 0.549 5.878 10252 Z= 0.309 Chirality : 0.034 0.115 1156 Planarity : 0.004 0.043 940 Dihedral : 27.513 144.609 2010 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.78 % Allowed : 17.66 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.36), residues: 580 helix: 0.52 (0.33), residues: 274 sheet: -0.48 (0.52), residues: 104 loop : -0.82 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 8 PHE 0.011 0.001 PHE A 124 TYR 0.009 0.002 TYR B 121 ARG 0.003 0.000 ARG B 123 Details of bonding type rmsd hydrogen bonds : bond 0.04907 ( 317) hydrogen bonds : angle 3.53765 ( 832) metal coordination : bond 0.00283 ( 16) metal coordination : angle 2.81108 ( 24) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00354 ( 7202) covalent geometry : angle 0.53283 (10226) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 1.200 Fit side-chains REVERT: A 28 ARG cc_start: 0.8985 (tpt90) cc_final: 0.8543 (tpt-90) REVERT: A 42 GLU cc_start: 0.7787 (pt0) cc_final: 0.7389 (pt0) REVERT: C 17 ARG cc_start: 0.8190 (mmt180) cc_final: 0.6895 (ttp-110) REVERT: B 30 GLN cc_start: 0.7836 (tt0) cc_final: 0.7383 (tt0) REVERT: D 23 THR cc_start: 0.7717 (p) cc_final: 0.7451 (t) REVERT: D 30 GLN cc_start: 0.7784 (tt0) cc_final: 0.7484 (mt0) outliers start: 14 outliers final: 10 residues processed: 108 average time/residue: 0.4865 time to fit residues: 66.8622 Evaluate side-chains 110 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 56 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.197378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131482 restraints weight = 8103.260| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.77 r_work: 0.3266 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7218 Z= 0.145 Angle : 0.539 6.576 10252 Z= 0.304 Chirality : 0.034 0.137 1156 Planarity : 0.004 0.043 940 Dihedral : 27.341 144.481 2010 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.18 % Allowed : 19.84 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.36), residues: 580 helix: 0.76 (0.33), residues: 274 sheet: -0.40 (0.52), residues: 104 loop : -0.77 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 8 PHE 0.009 0.001 PHE A 124 TYR 0.009 0.001 TYR D 121 ARG 0.002 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.04720 ( 317) hydrogen bonds : angle 3.45908 ( 832) metal coordination : bond 0.00253 ( 16) metal coordination : angle 2.64213 ( 24) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00316 ( 7202) covalent geometry : angle 0.52392 (10226) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.894 Fit side-chains REVERT: A 28 ARG cc_start: 0.8979 (tpt90) cc_final: 0.8531 (tpt-90) REVERT: A 42 GLU cc_start: 0.7729 (pt0) cc_final: 0.7330 (pt0) REVERT: C 17 ARG cc_start: 0.8165 (mmt180) cc_final: 0.6833 (ttp-110) REVERT: B 23 THR cc_start: 0.7548 (p) cc_final: 0.7248 (t) REVERT: B 30 GLN cc_start: 0.7782 (tt0) cc_final: 0.7379 (tt0) REVERT: D 23 THR cc_start: 0.7690 (p) cc_final: 0.7432 (t) REVERT: D 30 GLN cc_start: 0.7755 (tt0) cc_final: 0.7500 (mt0) outliers start: 11 outliers final: 9 residues processed: 108 average time/residue: 0.3072 time to fit residues: 41.1382 Evaluate side-chains 107 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.195868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.129466 restraints weight = 8150.208| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.76 r_work: 0.3234 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7218 Z= 0.176 Angle : 0.562 6.658 10252 Z= 0.313 Chirality : 0.034 0.118 1156 Planarity : 0.004 0.044 940 Dihedral : 27.368 144.189 2010 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.18 % Allowed : 20.04 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.36), residues: 580 helix: 0.70 (0.32), residues: 274 sheet: -0.43 (0.52), residues: 104 loop : -0.68 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 8 PHE 0.012 0.001 PHE A 124 TYR 0.007 0.002 TYR B 121 ARG 0.003 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.04797 ( 317) hydrogen bonds : angle 3.53093 ( 832) metal coordination : bond 0.00318 ( 16) metal coordination : angle 2.84041 ( 24) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00401 ( 7202) covalent geometry : angle 0.54603 (10226) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.888 Fit side-chains REVERT: A 28 ARG cc_start: 0.8969 (tpt90) cc_final: 0.8520 (tpt-90) REVERT: A 42 GLU cc_start: 0.7766 (pt0) cc_final: 0.7439 (pt0) REVERT: C 17 ARG cc_start: 0.8184 (mmt180) cc_final: 0.6910 (ttp-110) REVERT: B 23 THR cc_start: 0.7576 (p) cc_final: 0.7267 (t) REVERT: B 30 GLN cc_start: 0.7791 (tt0) cc_final: 0.7386 (tt0) REVERT: D 23 THR cc_start: 0.7691 (p) cc_final: 0.7422 (t) REVERT: D 30 GLN cc_start: 0.7783 (tt0) cc_final: 0.7507 (mt0) outliers start: 11 outliers final: 9 residues processed: 105 average time/residue: 0.3944 time to fit residues: 52.1401 Evaluate side-chains 106 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.197703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131568 restraints weight = 8249.968| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.72 r_work: 0.3266 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7218 Z= 0.144 Angle : 0.545 7.639 10252 Z= 0.306 Chirality : 0.033 0.118 1156 Planarity : 0.004 0.043 940 Dihedral : 27.172 143.837 2010 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.38 % Allowed : 19.84 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.36), residues: 580 helix: 0.84 (0.33), residues: 274 sheet: -0.36 (0.52), residues: 104 loop : -0.66 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 8 PHE 0.009 0.001 PHE A 124 TYR 0.009 0.001 TYR B 121 ARG 0.002 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 317) hydrogen bonds : angle 3.52100 ( 832) metal coordination : bond 0.00232 ( 16) metal coordination : angle 2.60674 ( 24) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00314 ( 7202) covalent geometry : angle 0.53122 (10226) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.540 Fit side-chains REVERT: A 28 ARG cc_start: 0.8964 (tpt90) cc_final: 0.8514 (tpt-90) REVERT: A 42 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7359 (pt0) REVERT: C 17 ARG cc_start: 0.8172 (mmt180) cc_final: 0.6892 (ttp-110) REVERT: B 23 THR cc_start: 0.7555 (p) cc_final: 0.7261 (t) REVERT: B 30 GLN cc_start: 0.7766 (tt0) cc_final: 0.7355 (tt0) REVERT: D 23 THR cc_start: 0.7666 (p) cc_final: 0.7423 (t) REVERT: D 30 GLN cc_start: 0.7733 (tt0) cc_final: 0.7482 (mt0) outliers start: 12 outliers final: 10 residues processed: 108 average time/residue: 0.2754 time to fit residues: 37.4920 Evaluate side-chains 108 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.0040 chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.197348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.131125 restraints weight = 8383.214| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.75 r_work: 0.3257 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7218 Z= 0.151 Angle : 0.555 7.848 10252 Z= 0.311 Chirality : 0.034 0.115 1156 Planarity : 0.004 0.043 940 Dihedral : 27.159 143.739 2010 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.18 % Allowed : 19.64 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.36), residues: 580 helix: 0.83 (0.32), residues: 274 sheet: -0.34 (0.52), residues: 104 loop : -0.64 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 8 PHE 0.010 0.001 PHE A 124 TYR 0.008 0.001 TYR B 121 ARG 0.002 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.04542 ( 317) hydrogen bonds : angle 3.55144 ( 832) metal coordination : bond 0.00268 ( 16) metal coordination : angle 2.66252 ( 24) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00334 ( 7202) covalent geometry : angle 0.54103 (10226) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.623 Fit side-chains REVERT: A 28 ARG cc_start: 0.8973 (tpt90) cc_final: 0.8518 (tpt-90) REVERT: A 42 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7366 (pt0) REVERT: B 23 THR cc_start: 0.7575 (p) cc_final: 0.7283 (t) REVERT: B 30 GLN cc_start: 0.7769 (tt0) cc_final: 0.7364 (tt0) REVERT: D 23 THR cc_start: 0.7675 (p) cc_final: 0.7434 (t) REVERT: D 30 GLN cc_start: 0.7727 (tt0) cc_final: 0.7487 (mt0) outliers start: 11 outliers final: 10 residues processed: 104 average time/residue: 0.2524 time to fit residues: 32.8513 Evaluate side-chains 111 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 7 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 34 optimal weight: 0.0070 chunk 20 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.197240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131994 restraints weight = 8234.133| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.72 r_work: 0.3268 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7218 Z= 0.157 Angle : 0.555 7.389 10252 Z= 0.310 Chirality : 0.034 0.117 1156 Planarity : 0.004 0.043 940 Dihedral : 27.132 143.607 2010 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.78 % Allowed : 19.05 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.36), residues: 580 helix: 0.66 (0.32), residues: 276 sheet: -0.34 (0.52), residues: 104 loop : -0.53 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 8 PHE 0.010 0.001 PHE A 124 TYR 0.008 0.001 TYR B 121 ARG 0.002 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.04557 ( 317) hydrogen bonds : angle 3.56864 ( 832) metal coordination : bond 0.00287 ( 16) metal coordination : angle 2.68979 ( 24) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00349 ( 7202) covalent geometry : angle 0.53993 (10226) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4541.25 seconds wall clock time: 84 minutes 6.41 seconds (5046.41 seconds total)